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Display units: line lists (spacetelescope#2148)
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* BaseSpectrumVerticalLine to inherit unit-support from PluginMark
* convert units on internal rest value
* code cleanup
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@kecnry @rosteen
kecnry authored and rosteen committed May 11, 2023
1 parent ed8503a commit d467bde
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Showing 3 changed files with 91 additions and 89 deletions.
4 changes: 2 additions & 2 deletions jdaviz/configs/specviz/plugins/line_analysis/line_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -530,8 +530,8 @@ def _uncertainty(result):
def _compute_redshift_for_selected_line(self):
index = self.line_items.index(self.selected_line)
line_mark = self.line_marks[index]
rest_value = (line_mark.rest_value * line_mark._x_unit).to_value(u.AA,
equivalencies=u.spectral())
rest_value = (line_mark.rest_value * line_mark.xunit).to_value(u.AA,
equivalencies=u.spectral())
return (self.results_centroid - rest_value) / rest_value

@observe('sync_identify')
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3 changes: 3 additions & 0 deletions jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,9 @@ def user_api(self):
def _on_glue_x_display_unit_changed(self, x_unit):
if x_unit is None:
return
if x_unit == 'deg' and self.app.config == 'cubeviz':
# original unit during init can be deg (before axis is set correctly)
return
self.spectrum_viewer.set_plot_axes()
if x_unit != self.spectral_unit.selected:
x_unit = _valid_glue_display_unit(x_unit, self.spectrum_viewer, 'x')
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173 changes: 86 additions & 87 deletions jdaviz/core/marks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,11 +59,75 @@ def _update_counts(self, *args):
self.right.text = [f'{oob_right} \u25b6' if oob_right > 0 else '']


class BaseSpectrumVerticalLine(Lines, HubListener):
class PluginMark():
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.xunit = None
self.yunit = None
# whether to update existing marks when global display units are changed
self.auto_update_units = True
self.hub.subscribe(self, GlobalDisplayUnitChanged,
handler=self._on_global_display_unit_changed)

if self.xunit is None:
self.set_x_unit()
if self.yunit is None:
self.set_y_unit()

@property
def hub(self):
return self.viewer.hub

def update_xy(self, x, y):
self.x = np.asarray(x)
self.y = np.asarray(y)

def append_xy(self, x, y):
self.x = np.append(self.x, x)
self.y = np.append(self.y, y)

def set_x_unit(self, unit=None):
if unit is None:
if not hasattr(self.viewer.state, 'x_display_unit'):
return
unit = self.viewer.state.x_display_unit
unit = u.Unit(unit)
if self.xunit is not None:
x = (self.x * self.xunit).to_value(unit, u.spectral())
self.xunit = unit
self.x = x
self.xunit = unit

def set_y_unit(self, unit=None):
if unit is None:
if not hasattr(self.viewer.state, 'y_display_unit'):
return
unit = self.viewer.state.y_display_unit
unit = u.Unit(unit)
if self.yunit is not None:
self.y = (self.y * self.yunit).to_value(unit)
self.yunit = unit

def _on_global_display_unit_changed(self, msg):
if not self.auto_update_units:
return
if self.viewer.__class__.__name__ in ['SpecvizProfileView', 'CubevizProfileView']:
axis_map = {'spectral': 'x', 'flux': 'y'}
elif self.viewer.__class__.__name__ == 'MosvizProfile2DView':
axis_map = {'spectral': 'x'}
else:
return
axis = axis_map.get(msg.axis, None)
if axis is not None:
getattr(self, f'set_{axis}_unit')(msg.unit)

def clear(self):
self.update_xy([], [])


class BaseSpectrumVerticalLine(Lines, PluginMark, HubListener):
def __init__(self, viewer, x, **kwargs):
# we'll store the current units so that we can automatically update the
# positioning on a change to the x-units
self._x_unit = viewer.state.reference_data.get_object(cls=Spectrum1D).spectral_axis.unit
self.viewer = viewer

# the location of the marker will need to update automatically if the
# underlying data changes (through a unit conversion, for example)
Expand All @@ -84,14 +148,14 @@ def _update_reference_data(self, reference_data):

def _update_data(self, x_all):
# the x-units may have changed. We want to convert the internal self.x
# from self._x_unit to the new units (x_all.unit)
# from self.xunit to the new units (x_all.unit)
new_unit = x_all.unit
if new_unit == self._x_unit:
if new_unit == self.xunit:
return
old_quant = self.x[0]*self._x_unit
old_quant = self.x[0]*self.xunit
x = old_quant.to_value(x_all.unit, equivalencies=u.spectral())
self.x = [x, x]
self._x_unit = new_unit
self.xunit = new_unit


class SpectralLine(BaseSpectrumVerticalLine):
Expand All @@ -111,7 +175,7 @@ def __init__(self, viewer, rest_value, redshift=0, name=None, **kwargs):
# setting redshift will set self.x and enable the obs_value property,
# but to do that we need x_unit set first (would normally be assigned
# in the super init)
self._x_unit = viewer.state.reference_data.get_object(cls=Spectrum1D).spectral_axis.unit
self.xunit = u.Unit(viewer.state.x_display_unit)
self.redshift = redshift

viewer.session.hub.subscribe(self, LineIdentifyMessage,
Expand All @@ -132,23 +196,28 @@ def rest_value(self):
def obs_value(self):
return self.x[0]

def set_x_unit(self, unit=None):
prev_unit = self.xunit
super().set_x_unit(unit=unit)
self._rest_value = (self._rest_value * prev_unit).to_value(unit, u.spectral())

@property
def redshift(self):
return self._redshift

@redshift.setter
def redshift(self, redshift):
self._redshift = redshift
if str(self._x_unit.physical_type) == 'length':
if str(self.xunit.physical_type) == 'length':
obs_value = self._rest_value*(1+redshift)
elif str(self._x_unit.physical_type) == 'frequency':
elif str(self.xunit.physical_type) == 'frequency':
obs_value = self._rest_value/(1+redshift)
else:
# catch all for anything else (wavenumber, energy, etc)
rest_angstrom = (self._rest_value*self._x_unit).to_value(u.Angstrom,
equivalencies=u.spectral())
rest_angstrom = (self._rest_value*self.xunit).to_value(u.Angstrom,
equivalencies=u.spectral())
obs_angstrom = rest_angstrom*(1+redshift)
obs_value = (obs_angstrom*u.Angstrom).to_value(self._x_unit,
obs_value = (obs_angstrom*u.Angstrom).to_value(self.xunit,
equivalencies=u.spectral())
self.x = [obs_value, obs_value]

Expand All @@ -169,14 +238,14 @@ def _process_identify_change(self, msg):

def _update_data(self, x_all):
new_unit = x_all.unit
if new_unit == self._x_unit:
if new_unit == self.xunit:
return

old_quant = self._rest_value*self._x_unit
old_quant = self._rest_value*self.xunit
self._rest_value = old_quant.to_value(new_unit, equivalencies=u.spectral())
# re-compute self.x from current redshift (instead of converting that as well)
self.redshift = self._redshift
self._x_unit = new_unit
self.xunit = new_unit


class SliceIndicatorMarks(BaseSpectrumVerticalLine, HubListener):
Expand Down Expand Up @@ -485,76 +554,6 @@ def _on_shadowing_changed(self, change):
self._update_align()


class PluginMark():
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.xunit = None
self.yunit = None
# whether to update existing marks when global display units are changed
self.auto_update_units = True
self.hub.subscribe(self, GlobalDisplayUnitChanged,
handler=self._on_global_display_unit_changed)
self._update_units()

@property
def hub(self):
return self.viewer.hub

def update_xy(self, x, y):
self.x = np.asarray(x)
self.y = np.asarray(y)

def append_xy(self, x, y):
self.x = np.append(self.x, x)
self.y = np.append(self.y, y)

def _update_units(self):
if not self.auto_update_units:
return
if self.xunit is None:
self.set_x_unit()
if self.yunit is None:
self.set_y_unit()

def set_x_unit(self, unit=None):
if unit is None:
if not hasattr(self.viewer.state, 'x_display_unit'):
return
unit = self.viewer.state.x_display_unit
unit = u.Unit(unit)
if self.xunit is not None:
x = (self.x * self.xunit).to_value(unit, u.spectral())
self.xunit = unit
self.x = x
self.xunit = unit

def set_y_unit(self, unit=None):
if unit is None:
if not hasattr(self.viewer.state, 'y_display_unit'):
return
unit = self.viewer.state.y_display_unit
unit = u.Unit(unit)
if self.yunit is not None:
self.y = (self.y * self.yunit).to_value(unit)
self.yunit = unit

def _on_global_display_unit_changed(self, msg):
if not self.auto_update_units:
return
if self.viewer.__class__.__name__ in ['SpecvizProfileView', 'CubevizProfileView']:
axis_map = {'spectral': 'x', 'flux': 'y'}
elif self.viewer.__class__.__name__ == 'MosvizProfile2DView':
axis_map = {'spectral': 'x'}
else:
return
axis = axis_map.get(msg.axis, None)
if axis is not None:
getattr(self, f'set_{axis}_unit')(msg.unit)

def clear(self):
self.update_xy([], [])


class LinesAutoUnit(PluginMark, Lines, HubListener):
def __init__(self, viewer, *args, **kwargs):
self.viewer = viewer
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